PAPi

Version: 1.18.0

Website

https://www.bioconductor.org/packages/release/bioc/html/PAPi.html

Description

Pathway Activity Profiling (PAPi) is a Bioconductor package which compares the activity of pathways between different biological conditions, using KEGG pathways and metabolite intensities. Activity scores (AS) are generated for each pathway and these can be compared using PCA, t-tests or ANOVA. These are calculated from the percentage of detected metabolites in the pathway and their intensities and are the normalised to the number of metabolites in the pathway. A dataframe of the KEGG codes of identified compounds and their abundances is the initial input. It is assumed that data have been appropriately normalised and transformed before this stage.

Functionality

• Pathway Analysis

Instrument Data Type

Approaches

Computer Skills

Advanced

Software Type

• R Package

Interface

• Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

R (≥ 2.15.2), svDialogs, KEGGREST

Input Formats - Open

data.frame

Input Formats - Proprietary

N/A

Published

2013

Last Updated

2017

License

GPL (≥ 2)

Paper

http://www.ncbi.nlm.nih.gov/pubmed/20929912

PMID

20929912